The Mass Spectrometry Core will provide support for all projects (1-4) with state-of-the-art mass spectrometry. The MS Core will work closely with the Protein Purification Core. The BUSM MS Resource is an NIH- NCRR Research Resource and has available electrospray ionization (ESI) on triple quadrupole, quadrupole orthogonal time-of-flight, and ion cyclotron resonance Fourier transform mass spectrometers, and ultraviolet and infrared matrix-assisted laser desorption/ionization (MALDI) on quadrupole orthogonal time-of-flight, reflectron time-of- flight and ion cyclotron resonance Fourier transform mass spectrometers, as well as a highly trained staff and commitment to the development and application of MS methodology for biopolymer structural analysis. Studies will include protein (and other biopolymer) fractions separated by prior or on-line chromatography, as well as amyloid fibrils, and sports from SDS/PAGE and IEF gels that will be subjected to in-gel digestion prior to MS and multi-stage MS analysis. Results will be compared to protein sequences predicted from gene sequences and with on-line databases and/or interpreted manually. This Core will support Project I with molecular weight determinations and sequence verifications of expressed proteins, as well as assessment of purity and elucidation of variations in amino acid sequence and post-translational modifications, including structural determinations of and O- linked glycans. For Project 2, the same types of information will be provided for clinically- derived proteins. Both proteins and glycosaminoglycans will be analyzed for Project 3. Tumor peptide immunogens in Project 4 will e identified by MS and MS/MS.